Contacts of the helix formed by residues 323 - 348 (chain D) in PDB entry 1U3Q
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 323 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D GLU 4.0 0.4 + - - -
322D LEU* 1.3 75.6 - - - +
324D LEU* 1.3 65.0 + - - +
325D PHE* 3.4 9.7 + - - +
326D ASP* 2.9 40.0 + - - +
327D GLN* 3.0 10.4 + - - +
422D SER* 3.3 15.8 + - - -
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Residues in contact with LEU 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D VAL 5.6 0.9 - - - +
322D LEU 5.0 0.9 - - - +
323D SER* 1.3 72.5 - - - +
325D PHE* 1.3 69.5 + - + +
327D GLN* 3.4 24.3 + - - +
328D VAL* 3.0 35.4 + - + +
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Residues in contact with PHE 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D SER* 3.1 7.9 + - - +
324D LEU* 1.3 85.6 - - + +
326D ASP* 1.3 61.1 + - - +
328D VAL* 4.1 5.5 - - + +
329D ARG* 2.9 31.7 + - - +
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Residues in contact with ASP 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322D LEU* 4.2 13.7 - - + -
323D SER* 2.9 22.1 + - - +
325D PHE* 1.3 77.0 - - - +
327D GLN* 1.3 57.3 + - - +
329D ARG* 3.0 30.5 + - - +
330D LEU* 2.8 43.3 + - + +
409D SER* 5.0 1.4 + - - -
411D TYR 4.5 6.5 - - - +
422D SER* 2.7 33.0 + - - -
423D SER* 5.4 1.5 + - - -
426D LEU* 6.0 4.7 - - + +
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Residues in contact with GLN 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D LYS* 4.9 8.0 - - - +
319D PHE* 3.3 58.2 + - + +
320D VAL* 3.3 19.4 + - - +
322D LEU* 2.8 28.9 + - + -
323D SER 3.0 9.6 + - - +
324D LEU* 3.4 29.6 + - - +
326D ASP* 1.3 77.2 - - - +
328D VAL* 1.3 63.1 + - + +
330D LEU* 3.7 1.4 + - - +
331D LEU* 3.2 31.5 + - + +
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Residues in contact with VAL 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324D LEU* 3.0 22.1 + - + +
325D PHE* 4.2 5.8 - - + +
327D GLN* 1.3 76.7 - - + +
329D ARG* 1.3 60.1 + - - +
331D LEU* 3.8 6.2 - - + +
332D GLU* 2.8 65.9 + - + +
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Residues in contact with ARG 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D PHE 2.9 20.2 + - - +
326D ASP* 3.0 26.6 + - - +
328D VAL* 1.3 75.2 - - - +
330D LEU* 1.3 65.1 + - + +
332D GLU* 4.1 8.4 - - - +
333D SER* 3.1 29.2 + - - -
409D SER* 3.8 20.9 + - - +
410D MET 5.5 0.2 - - - +
411D TYR 2.6 30.8 + - - +
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Residues in contact with LEU 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D PHE* 4.0 13.0 - - + -
322D LEU* 3.6 31.2 - - + -
326D ASP* 2.8 26.6 + - + +
327D GLN 3.9 3.6 - - - +
329D ARG* 1.3 75.2 - - - +
331D LEU* 1.3 63.2 + - - +
333D SER* 3.3 0.6 + - - -
334D CYS* 3.3 19.6 + - - -
405D LEU* 3.6 28.9 - - + +
406D LEU* 4.4 13.5 - - + +
408D SER* 3.4 14.2 + - - +
409D SER* 3.5 33.7 - - - +
426D LEU* 3.9 14.4 - - + -
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Residues in contact with LEU 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D MET* 4.1 28.5 - - + +
310D ILE* 4.4 26.2 - - + -
312D TRP* 5.3 0.4 - - + -
313D ALA* 3.9 22.9 - - + -
319D PHE* 4.0 17.3 - - + -
327D GLN* 3.2 22.2 + - + +
328D VAL* 3.9 6.5 - - + +
330D LEU* 1.3 79.1 - - - +
332D GLU* 1.3 63.4 + - + +
333D SER 3.1 0.3 + - - -
334D CYS* 4.6 0.7 - - - -
335D TRP* 3.0 29.8 + - - +
405D LEU* 3.9 14.1 - - + -
494D MET* 4.0 13.5 - - + -
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Residues in contact with GLU 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D VAL* 2.8 50.9 + - + +
329D ARG* 4.3 7.8 - - - +
331D LEU* 1.3 71.6 - - + +
333D SER* 1.3 57.1 + - - +
334D CYS 3.6 0.2 - - - -
335D TRP* 3.2 19.9 + - - -
473D MET* 5.2 2.3 - - - +
493D GLU* 4.6 9.9 - - - +
494D MET* 3.9 28.4 - - + +
497D ALA* 3.3 33.9 - - + +
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Residues in contact with SER 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329D ARG* 3.1 21.2 + - - -
330D LEU 3.8 2.9 - - - -
331D LEU 3.1 1.2 - - - -
332D GLU* 1.3 80.0 - - - +
334D CYS* 1.3 56.7 + - - +
335D TRP* 4.8 1.3 - - - -
337D GLU* 4.8 4.3 - - - +
408D SER* 3.3 29.4 + - - -
409D SER* 6.3 0.4 - - - -
466D ARG* 5.4 6.1 + - - -
473D MET* 5.7 4.3 - - - +
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Residues in contact with CYS 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330D LEU 3.3 17.5 + - - -
331D LEU* 4.3 3.4 - - - -
333D SER* 1.3 78.1 - - - +
335D TRP* 1.3 66.9 + - - +
336D MET 3.4 3.1 - - - -
337D GLU* 3.2 27.8 + - - +
338D VAL* 3.0 35.6 + - - +
404D ILE* 4.0 3.6 - - + +
405D LEU* 3.7 28.7 - - - -
408D SER* 3.7 16.4 - - - -
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Residues in contact with TRP 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D ALA* 5.0 1.3 - - + -
306D LEU* 3.9 22.0 - - + -
309D MET* 3.2 24.8 - - + +
331D LEU 3.0 14.1 + - - +
332D GLU* 3.2 27.6 + - - -
333D SER 4.8 1.1 - - - -
334D CYS* 1.3 76.3 - - - +
336D MET* 1.3 99.8 + - + +
338D VAL 3.1 2.8 + - - -
339D LEU* 2.9 37.3 + - + +
473D MET* 3.2 40.0 - - + +
476D LEU* 4.3 2.0 - - + -
491D LEU* 3.6 30.1 - - + -
494D MET* 3.6 41.7 + - + +
495D LEU* 4.1 14.8 - - + -
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Residues in contact with MET 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D ALA* 6.3 0.7 - - + -
334D CYS 3.4 0.8 - - - -
335D TRP* 1.3 105.9 - - + +
337D GLU* 1.3 55.3 + - - +
339D LEU* 3.0 20.1 + - + +
340D MET* 2.8 42.8 + - - +
469D SER* 3.0 36.1 - - - +
472D GLY* 4.0 22.9 - - - +
473D MET* 3.9 18.4 - - + +
476D LEU* 4.9 4.7 - - + -
501D 272 3.9 36.6 - - + -
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Residues in contact with GLU 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333D SER 4.8 2.0 - - - +
334D CYS* 3.2 23.0 + - - +
336D MET* 1.3 76.4 - - - +
338D VAL* 1.3 58.6 + - - +
340D MET* 3.3 1.6 + - - +
341D MET* 2.9 31.1 + - - +
404D ILE* 3.2 28.8 - - + +
408D SER* 5.1 0.3 - - - -
462D LEU 4.6 1.7 - - - +
465D VAL* 3.8 16.4 - - + +
466D ARG* 2.3 60.1 + - - +
469D SER* 3.4 24.8 + - - +
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Residues in contact with VAL 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D MET* 3.5 22.9 - - + -
312D TRP* 3.9 31.9 - - + -
334D CYS* 3.0 32.6 + - - +
335D TRP 3.3 7.6 - - - +
337D GLU* 1.3 76.9 - - - +
339D LEU* 1.3 62.3 + - + +
341D MET* 3.5 6.3 + - - +
342D GLY* 3.1 18.4 + - - -
401D LYS* 4.3 22.7 - - + +
404D ILE* 4.3 11.7 - - + -
405D LEU 4.8 0.4 - - - +
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Residues in contact with LEU 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D ALA* 4.0 18.6 - - + +
305D GLU* 3.7 39.8 - - + +
306D LEU* 5.0 1.3 - - + +
309D MET* 3.9 17.0 - - + -
335D TRP* 2.9 39.6 + - + +
336D MET* 3.0 14.8 + - - +
338D VAL* 1.3 78.3 - - + +
340D MET* 1.3 58.2 + - - +
342D GLY* 3.0 4.8 + - - -
343D LEU 2.8 22.2 + - - -
346D ARG* 4.6 0.9 + - - -
501D 272 3.7 36.8 - - + +
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Residues in contact with MET 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D MET* 2.8 30.7 + - + +
337D GLU* 3.9 4.3 - - - +
339D LEU* 1.3 69.2 - - - +
341D MET* 1.3 65.3 + - - +
343D LEU* 3.0 9.4 + - - +
344D MET* 2.9 35.6 + - + +
376D ILE* 4.3 2.9 - - + -
380D LEU* 3.8 26.2 - - + -
465D VAL* 4.5 4.0 - - + +
468D ALA* 3.0 33.0 - - - +
469D SER* 3.5 23.6 - - - -
472D GLY* 4.1 3.6 - - - -
501D 272 3.5 43.1 - - - +
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Residues in contact with MET 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D GLU 2.9 18.1 + - - +
338D VAL* 3.7 6.1 - - - +
340D MET* 1.3 75.6 - - - +
342D GLY* 1.3 63.2 + - - +
344D MET* 3.4 9.0 + - + -
345D TRP* 3.1 22.0 + - - +
387D PHE* 3.8 40.8 - - + -
392D LEU* 3.8 25.1 - - + -
397D TYR* 3.8 19.0 - - + -
400D VAL* 4.2 20.0 - - + -
401D LYS* 4.8 8.7 - - + -
404D ILE* 3.9 20.2 - - + -
462D LEU* 4.7 0.2 - - - -
465D VAL* 4.4 12.9 - - + +
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Residues in contact with GLY 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D VAL 3.1 11.3 + - - -
339D LEU* 3.0 9.1 + - - -
341D MET* 1.3 78.7 - - - +
343D LEU* 1.3 60.6 + - - +
345D TRP* 3.4 2.6 + - - +
346D ARG* 3.2 41.0 + - - +
397D TYR* 3.8 20.7 + - - -
401D LYS* 5.4 1.8 - - - +
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Residues in contact with LEU 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D LEU 2.8 12.8 + - - +
340D MET* 3.0 9.6 + - - +
342D GLY* 1.3 75.3 - - - +
344D MET* 1.3 63.6 + - + +
346D ARG* 3.3 14.1 + - - +
347D SER* 2.9 41.7 + - - +
354D LEU* 4.2 15.7 - - + -
355D ILE 3.7 25.8 - - - +
356D PHE* 3.8 20.6 - - + +
380D LEU* 3.7 38.6 - - + -
501D 272 3.7 19.5 - - + +
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Residues in contact with MET 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340D MET* 2.9 26.8 + - + +
341D MET* 3.8 8.1 - - + +
343D LEU* 1.3 76.3 - - + +
345D TRP* 1.3 67.1 + - - +
347D SER* 2.9 2.9 + - - -
348D ILE* 2.8 25.0 + - - +
380D LEU* 3.7 29.6 - - + +
383D THR* 3.7 39.5 - - + +
384D THR* 3.2 32.3 - - - +
387D PHE* 3.8 24.7 - - + -
465D VAL* 4.2 17.9 - - + -
468D ALA* 4.8 2.2 - - + -
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Residues in contact with TRP 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341D MET* 3.1 9.4 + - + +
342D GLY 3.6 4.0 - - - +
344D MET* 1.3 75.3 - - - +
346D ARG* 1.3 70.0 + - + +
348D ILE* 3.0 45.7 - - + +
392D LEU* 3.5 40.4 - - + -
393D GLN* 4.0 2.9 - - - -
394D HIS* 3.3 56.7 + + + -
397D TYR* 3.4 48.2 - + + -
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Residues in contact with ARG 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D HIS* 5.1 18.4 - - + +
305D GLU* 4.0 15.3 + - - -
339D LEU 4.9 0.2 + - - -
342D GLY* 3.2 30.6 + - - +
343D LEU* 3.6 21.7 - - - +
344D MET 3.2 0.2 - - - -
345D TRP* 1.3 87.4 - - + +
347D SER* 1.3 59.8 + - - +
348D ILE* 3.4 0.8 + - - +
349D ASP* 4.7 1.0 + - - +
350D HIS* 3.8 11.3 + - - -
355D ILE* 3.1 43.1 + - + +
356D PHE* 3.2 25.8 + - - +
357D ALA* 5.4 2.5 - - - +
358D PRO* 5.8 2.9 - - - -
397D TYR* 5.4 1.2 + - - -
501D 272 3.4 23.0 + - - -
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Residues in contact with SER 347 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343D LEU* 2.9 19.7 + - - +
344D MET 2.9 5.8 + - - -
346D ARG* 1.3 74.3 - - - +
348D ILE* 1.3 66.9 + - - +
349D ASP 3.2 2.9 - - - -
350D HIS 2.9 15.7 + - - -
353D LYS 3.5 16.6 - - - -
354D LEU* 3.5 3.6 - - - -
355D ILE* 2.7 33.7 + - - -
384D THR* 3.9 15.9 - - - -
388D ARG* 3.2 11.3 + - - -
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Residues in contact with ILE 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344D MET 2.8 10.3 + - - +
345D TRP* 3.0 39.7 - - + +
346D ARG 3.4 0.6 - - - -
347D SER* 1.3 77.2 - - - +
349D ASP* 1.3 77.0 + - - +
384D THR* 4.2 8.7 - - - +
387D PHE* 3.8 16.6 - - + +
388D ARG* 2.8 48.1 + - + +
391D LYS* 4.8 1.6 - - - -
392D LEU* 3.8 41.5 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il